You should also be getting a refund/credit on your MO taxes for any taxes withheld on your wages in MO; this will improve your net. Check your MO form NRI to ensure all the items correspond to what should be happening.
You should only be taxed in MO for those other income items and get a credit on your IL return for that tax paid to MO on those other income items.
On the IL return your tax liability will be a bit higher as you are resident IL but did not have IL taxes withheld on your pay. Again you are getting MO withheld taxes returned to you to mitigate.
Your military spouse's military pay will not be taxed in IL nor MO, so is not a factor.
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